Contacts of the helix formed by residues 77 - 85 (chain K) in PDB entry 6XAV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 77 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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729I ALA* 4.6 3.1 - - + -
755I LYS* 3.8 21.2 + - - +
756I TYR* 2.8 37.4 + - - +
766I ASN* 4.5 4.9 + - - +
767I GLN 5.5 1.6 - - - +
768I MET* 5.6 10.0 - - + +
69K SER 3.0 18.9 - - - +
70K THR* 4.3 2.3 - - - +
76K GLU* 1.3 76.4 - - - +
78K ILE* 1.3 75.1 + - - +
79K LEU 3.3 0.9 - - - -
80K GLU* 3.0 19.9 + - + +
81K ILE* 2.7 38.0 + - - +
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Residues in contact with ILE 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61K ILE* 4.4 19.1 - - + -
64K VAL* 3.7 26.0 - - + -
66K HIS 3.8 5.8 - - - +
67K GLU* 3.7 23.8 - - + +
69K SER* 3.3 33.9 - - - +
70K THR* 3.9 5.4 - - - -
71K LYS* 4.0 22.0 - - + +
74K VAL* 5.3 3.4 - - + -
77K ASP* 1.3 79.3 + - - +
79K LEU* 1.3 59.7 + - - +
81K ILE* 3.3 15.9 + - + +
82K LEU* 3.1 23.2 + - + +
171K LEU* 4.4 7.9 - - + -
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Residues in contact with LEU 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693I LEU* 3.8 23.6 - - + -
756I TYR* 3.3 28.3 - - + +
831I ILE* 3.8 28.5 - - + -
1057I LYS* 5.0 15.3 - - + +
67K GLU* 3.2 35.5 + - + +
68K TYR* 5.0 4.7 - - + -
77K ASP* 3.3 1.8 + - - -
78K ILE* 1.3 78.7 - - - +
80K GLU* 1.3 57.6 + - - +
82K LEU* 3.2 10.1 + - + +
83K LEU* 2.9 27.8 + - + +
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Residues in contact with GLU 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756I TYR* 5.0 0.2 + - - -
768I MET* 3.4 32.5 - - + +
76K GLU* 3.2 34.6 - - + +
77K ASP* 3.0 27.1 + - + +
79K LEU* 1.3 76.9 - - - +
81K ILE* 1.3 63.5 + - - +
83K LEU* 3.1 22.9 + - + +
84K ASN* 2.9 25.4 + - - +
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Residues in contact with ILE 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61K ILE* 4.6 11.9 - - + -
74K VAL* 4.2 22.9 - - + -
76K GLU* 4.3 11.9 - - + -
77K ASP 2.7 20.9 + - - +
78K ILE* 3.5 23.8 - - + +
79K LEU 3.2 0.2 - - - -
80K GLU* 1.3 73.2 - - - +
82K LEU* 1.3 61.1 + - + +
84K ASN* 2.8 25.1 - - - +
85K LEU* 3.1 28.1 + - + +
130K ILE* 4.5 13.9 - - + +
131K CYS* 4.3 11.4 - - + -
140K ILE* 5.0 7.6 - - + -
142K MET* 4.2 18.4 - - + -
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Residues in contact with LEU 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59K VAL* 3.7 30.7 - - + -
61K ILE* 4.8 7.4 - - + -
67K GLU* 3.6 31.0 - - + +
78K ILE 3.1 13.4 + - - +
79K LEU* 3.2 13.0 + - + +
81K ILE* 1.3 81.1 - - + +
83K LEU* 1.3 59.7 + - - +
84K ASN 3.6 0.2 - - - -
85K LEU* 4.1 8.1 - - + +
86K LYS* 3.9 8.0 + - - +
171K LEU* 4.0 32.3 - - + -
172K LEU 4.8 5.6 - - - +
173K VAL* 3.7 32.1 - - + +
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Residues in contact with LEU 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693I LEU* 3.7 35.9 - - + +
694I ARG* 3.5 40.4 - - + +
79K LEU* 2.9 15.4 + - + +
80K GLU* 3.1 19.7 + - + +
82K LEU* 1.3 78.3 - - - +
84K ASN* 1.3 66.2 + - + +
86K LYS* 3.4 23.0 - - + +
87K GLY 4.2 1.6 + - - -
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Residues in contact with ASN 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K GLU* 4.8 4.6 - - - +
80K GLU* 2.9 30.5 + - + +
81K ILE* 2.8 21.8 - - - +
83K LEU* 1.3 76.6 - - + +
85K LEU* 1.3 64.4 + - - +
86K LYS 3.2 1.9 + - - -
87K GLY* 3.5 5.7 + - - +
128K HIS* 2.9 32.4 + - + +
129K VAL 4.3 11.4 + - - +
130K ILE* 2.8 43.0 + - - +
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Residues in contact with LEU 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K VAL* 3.3 35.0 - - + +
59K VAL* 4.0 26.9 - - + -
81K ILE* 3.1 33.9 + - + +
82K LEU* 4.3 7.9 - - + +
83K LEU 3.4 0.2 - - - -
84K ASN* 1.3 82.6 + - - +
86K LYS* 1.3 64.8 + - - +
88K LEU* 3.4 15.8 - - + +
130K ILE* 3.7 31.9 - - + -
142K MET* 4.1 15.5 - - - -
144K ILE* 3.8 24.5 - - + -
173K VAL* 5.7 1.3 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il